gatk --java-options "-Xmx36g -XX:ParallelGCThreads=10" HaplotypeCaller \
        --input $1 \
        --output $3 \
        --reference ~/append-ssd/work/gencode.v46.pri.fa \
        --dbsnp ~/append-ssd/work/vcf/00-common_all.vcf.gz \
        --intervals $2 --verbosity WARNING \
        --dont-use-soft-clipped-bases --standard-min-confidence-threshold-for-calling 20
